Computational Tools for Modeling Protein Networks

Authors: Bergmann, Frank T.¹; Vallabhajosyula, Ravishankar R.¹; Sauro, Herbert M.¹

Source: Current Proteomics, Volume 3, Number 3, October 2006 , pp. 181-197(17)

Publisher: Bentham Science Publishers

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Abstract:

There are a large number of software packages available, both commercial and academic, to assist researchers in modeling protein networks. In this paper, we briefly review some of the more commonly used tools and focus on the current state of the Systems Biology Workbench (SBW), a modular framework that connects modeling and analysis applications, enabling tools to reuse each other's capabilities. We describe how users and developers perceive SBW and then describe the currently available SBW modules.

Keywords: Systems biology workbench; Java-based simulation and animation environment; Complex pathway simulator; Virtual cell; Systems biology markup language

Document Type: Research article

DOI: 10.2174/157016406779475380

Affiliations: 1: Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.

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